lecture_notes:05-15-2015
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lecture_notes:05-15-2015 [2015/05/18 15:02] gepoliano |
lecture_notes:05-15-2015 [2015/05/18 15:11] (current) gepoliano |
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| * Pre-processed adapter trimming | * Pre-processed adapter trimming | ||
| * Duplicate-removal is later than indexing | * Duplicate-removal is later than indexing | ||
| - | * One issue the group found: SW018 and 19, same library are optical PCR duplicates that should be removed | + | * One issue the group found: SW018 and 19, same library are optical PCR duplicates that should be removed |
| + | * The overall duplication level is a problem | ||
| + | * Each datset was generated independently | ||
| + | * Then, removing duplicates should be done apart for each dataset | ||
| + | * The dataset is very complicated - there is big duplication rate across the dataset the group has | ||
| + | * Merging indexes - planning on pulling some stats from the grin engine to pull information | ||
| + | * The wall time is large | ||
| + | * A variant file with the bubble pop counted the contigs | ||
| + | * The group is planning on using the mate-pair data | ||
| + | * Do adapter removal and index removal - using skewer | ||
| + | * | ||
lecture_notes/05-15-2015.1431961376.txt.gz · Last modified: 2015/05/18 15:02 by gepoliano
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